[Bioperl-l] error while remote blast against swissprot db

DeeGee gdorjee at hotmail.com
Sun Apr 15 20:40:22 EDT 2007


hi guys,
thanks for your replies, but i still don't understand why it doesn't work.
my input fasta sequence looks fine. here, take a look,

>gi|18676474|dbj|BAB84889.1| FLJ00134 protein [Homo sapiens]
HLSAQKASVGPESVSGLGTRTWPRVSCEVTVQCWPGCHLKVGGFKMAPWQGVGRRPWFLTWGPLCGAASVSPSMTVASSQ
QGWDCTAGRRWLGEGEIEALAQVSEFKTVLSFQGPAASPDGSSATRVPQDVTQGPGATGGKEDSGMIPLAGTAPGAEGPA
PGDSQAVRPYKQEPSSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHLLRHRQSHSGEKPHACPECGKAFRRKEHLRRHR
DTHPGSPGSPGPALRPLPAREKPHACCECGKTFYWREHLVRHRKTHSGARPFACWECGKGFGRREHVLRHQRIHGRAAAS
AQGAVAPGPDGGGPFPPWPLG

is it possible that the script is not being able to read the RemoteBlast.pm?
but the thing is, i can run the standalone blast on the command line,
although i've never been able the run the same with cgi module (by gettting
the input from an html textarea). i don't understand. i've been trying to
get the standalone running for a while now, and i also mentioned it in my
previous postings....but all in vain. i haven't got over it yet. 
any help or an example would be much appreciated.



Spiros Denaxas wrote:
> 
> Yep, it must be in the input file. The
> 
> $result->database_name()
> 
> function gets called on $result the result object.
> 
> The error you get,
> 
> Can't call method "database_name" on an undefined value at
> test1_remote_swissblast.pl line 41, <GEN4> line 31.
> 
> means the result object is not defined thus the function fails since
> there are no data to operate on.
> 
> Spiros
> 
> On 4/15/07, David Messina <dmessina at wustl.edu> wrote:
>> Hi DeeGee,
>>
>> Your script worked fine for me. Perhaps the problem is in your input
>> fasta file?
>>
>> Dave
>>
>> % perl test.pl AAC12660.fa
>> waiting... 5 units of time
>> waiting... 10 units of time
>> waiting... 15 units of time
>> database: Non-redundant SwissProt sequences
>> hit name is: sp|Q15750|TAB1_HUMAN
>> score is: 2413
>> hit name is: sp|Q8CF89|TAB1_MOUSE
>> score is: 2352
>> hit name is: sp|P49444|PP2C_PARTE
>> score is: 159
>> hit name is: sp|Q6ING9|PP2CK_XENLA
>> [...etc...]
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/error-while-remote-blast-against-swissprot-db-tf3577674.html#a10008507
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



More information about the Bioperl-l mailing list